Updated Annotation (v3) for the Phased Assembly of Atlantic Tetraploid Potato

February 17, 2023 - The Buell Lab at the University of Georgia is pleased to make available an updated set of genome annotation for the Atlantic genome assembly (ATL_v3). We generated transcript and functional annotations for the Atlantic genome (Hoopes et al. 2022) using mRNA-seq and Oxford Nanopore full-length cDNA libraries.

Note: the previous Atlantic v2.0 assembly and annotation can be found HERE.

JBrowse Genome Browser

• Genome browser for the Atlantic v3 assembly and annotation

Genome Assembly:

• ATL_v3.asm.fa.gz - Genome assembly for Atlantic - v3
• ATL_v3.asm.hm.fa.gz - Masked genome assembly for Atlantic - v3
• ATL_v3.asm.sm.fa.gz - Soft masked genome assembly for Atlantic - v3

Genome Annotation:

• High Confidence Gene Model Set
• ATL_v3.hc_gene_models.cdna.fa.gz - Transcript sequences (cDNA) of the high confidence gene models
• ATL_v3.hc_gene_models.cds.fa.gz - Coding sequences (CDS) of the high confidence gene models
• ATL_v3.hc_gene_models.pep.fa.gz - Protein sequences of the high confidence gene models
• ATL_v3.hc_gene_models.gff3.gz - High confidence gene models annotation in GFF3 format


• Representative High Confidence Gene Model Set

High confidence representative gene models are a subset of the high confidence gene model set. Each representative gene model is the isoform with the longest CDS at each locus.

• ATL_v3.hc_gene_models.repr.cdna.fa.gz - Transcript sequences (cDNA) of the the representative high confidence gene models
• ATL_v3.hc_gene_models.repr.cds.fa.gz - Coding sequences (CDS) of the representative high confidence gene models
• ATL_v3.hc_gene_models.repr.pep.fa.gz - Protein sequences of the representative high confidence gene models
• ATL_v3.hc_gene_models.repr.gff3.gz - Representative high confidence gene models annotation in GFF3 format


• Working Gene Model Set

The set of working gene models contains all loci and isoforms from the annotation pipeline and may include artifacts such as partial gene models.

• ATL_v3.working_models.cdna.fa.gz - Transcript sequences (cDNA) of the working gene models
• ATL_v3.working_models.cds.fa.gz - Coding sequences (CDS) of the working gene models
• ATL_v3.working_models.pep.fa.gz - Protein sequences of the working gene models
• ATL_v3.working_models.gff3.gz - Working gene models annotation in GFF3 format
• ATL_v3.functional_annotation.txt.gz - Functional annotation for the working gene models
• ATL_v3.working_models.go_slim.obo.gz - GO Slim annotation for the working gene models


• Representative Working Gene Model Set

The representative working gene models are a subset of the working gene model set. Each representative gene model is the isoform with the longest CDS at each locus.

• ATL_v3.working_models.repr.cdna.fa.gz - Transcript sequences (cDNA) of the representative working gene models
• ATL_v3.working_models.repr.cds.fa.gz - Coding sequences (CDS) of the representative working gene models
• ATL_v3.working_models.repr.pep.fa.gz - Protein sequences of the representative working gene models